Contacts of the helix formed by residues 407 - 423 (chain D) in PDB entry 4QGC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 407 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D SER* 1.3 82.5 + - - +
408D PRO* 1.3 73.7 - - - +
409D THR* 2.8 38.2 + - - -
410D GLU* 3.3 32.9 + - - +
411D ALA* 3.3 21.5 + - - +
440D GLN* 4.4 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C CYS* 6.0 0.2 - - - -
508C VAL* 5.2 5.6 - - + -
527C VAL* 3.4 41.1 - - + +
529C PRO* 4.2 24.9 - - + -
406D SER 3.4 6.0 - - - +
407D ASP* 1.3 95.5 - - - +
409D THR* 1.3 52.0 + - - +
411D ALA* 3.6 0.7 + - - +
412D THR* 2.7 36.6 + - - -
521D PHE* 4.4 13.9 - - + -
522D THR 4.6 1.1 - - - -
523D ASN* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D ASP* 2.8 14.4 + - - -
408D PRO* 1.3 74.8 - - - +
410D GLU* 1.3 59.7 + - - +
412D THR* 3.4 2.1 + - - -
413D ALA* 3.0 28.2 + - + +
437D SER* 4.8 8.3 - - - +
440D GLN* 3.5 27.6 - - + +
521D PHE* 3.8 24.4 - - - +
522D THR* 3.4 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D SER* 5.6 2.6 + - - -
407D ASP* 3.3 30.9 + - - +
409D THR* 1.3 77.2 - - - +
411D ALA* 1.3 58.0 + - - +
413D ALA* 3.3 4.3 + - - +
414D VAL* 3.0 35.0 + - + +
440D GLN* 3.2 24.6 + - + +
444D TYR* 4.5 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C ALA* 5.6 5.8 - - + +
422C ARG* 4.4 21.7 + - + +
423C CYS* 3.5 31.9 - - - -
525C MET* 5.6 1.4 - - - +
527C VAL* 4.5 9.6 - - + -
406D SER 6.1 0.7 - - - +
407D ASP 3.3 11.8 + - - +
408D PRO 3.9 4.7 - - - +
409D THR 3.3 0.2 - - - -
410D GLU* 1.3 78.9 - - - +
412D THR* 1.3 58.5 + - - +
414D VAL* 3.5 2.1 + - - +
415D GLY* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525C MET* 5.3 4.9 - - + -
527C VAL* 3.7 11.6 - - - +
408D PRO 2.7 22.7 + - - -
409D THR 3.6 4.9 - - - -
411D ALA* 1.3 76.2 - - - +
413D ALA* 1.3 60.2 + - - +
415D GLY* 3.4 1.6 + - - -
416D ALA* 2.9 28.1 + - - +
512D LEU* 3.7 24.2 - - + +
522D THR* 3.8 13.0 - - + +
523D ASN* 3.4 34.9 + - - +
524D THR 4.0 5.4 - - - +
525D MET* 4.2 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D THR* 3.0 18.1 + - + +
410D GLU 3.6 4.9 - - - +
411D ALA 3.3 0.2 - - - -
412D THR* 1.3 75.3 - - - +
414D VAL* 1.3 65.0 + - - +
416D ALA* 3.3 4.5 + - - +
417D VAL* 3.2 28.4 + - - +
437D SER 5.3 0.2 - - - +
440D GLN* 4.1 26.9 - - + +
441D VAL* 3.9 26.0 - - + +
444D TYR* 4.4 4.9 - - + -
512D LEU* 4.6 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C ARG* 3.5 42.2 - - - +
395D PHE* 4.3 6.4 - - + -
399D ARG* 4.3 14.6 - - + -
410D GLU* 3.0 19.5 + - + +
411D ALA* 3.8 4.3 - - - +
413D ALA* 1.3 75.0 - - - +
415D GLY* 1.3 58.4 + - - +
417D VAL* 3.3 5.7 + - - +
418D GLU* 2.9 31.6 + - - +
444D TYR* 3.4 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C GLY* 6.0 4.4 - - - -
418C GLU* 5.8 0.4 - - - -
419C ALA* 6.4 1.6 - - - -
422C ARG* 4.8 4.0 - - - +
525C MET* 5.1 7.0 - - - -
411D ALA 2.9 17.6 + - - -
412D THR* 3.7 2.5 - - - -
413D ALA 3.3 0.2 - - - -
414D VAL* 1.3 76.0 - - - +
416D ALA* 1.3 57.0 + - - +
418D GLU* 3.5 12.1 + - - +
419D ALA* 2.9 30.8 + - - +
525D MET* 3.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D THR 2.9 17.7 + - - +
413D ALA 3.6 5.6 - - - +
414D VAL 3.2 0.2 - - - -
415D GLY* 1.3 74.8 - - - +
417D VAL* 1.3 59.7 + - + +
419D ALA* 3.2 3.1 + - - +
420D SER* 2.8 28.6 + - - -
428D ILE* 4.2 9.6 - - + -
441D VAL* 5.1 0.7 - - + -
510D ILE* 3.8 14.9 - - + +
512D LEU* 3.7 32.3 - - + -
525D MET* 3.6 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D PHE* 3.6 29.6 - - + -
413D ALA 3.2 14.2 + - - +
414D VAL 3.8 6.1 - - - +
416D ALA* 1.3 71.9 - - - +
418D GLU* 1.3 65.3 + - - +
420D SER* 2.5 24.8 + - - -
421D PHE* 3.2 25.4 + - + -
428D ILE* 4.1 1.6 - - + -
441D VAL* 3.7 35.0 - - + +
444D TYR* 4.0 8.7 - - + -
446D PRO* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ARG* 5.8 1.2 + - - -
418C GLU* 3.2 31.7 - - - +
422C ARG* 2.6 45.3 + - - -
395D PHE* 3.5 26.6 - - + -
399D ARG* 2.7 23.9 + - - +
414D VAL* 2.9 14.8 + - - +
415D GLY* 3.6 7.3 - - - +
417D VAL* 1.3 75.5 - - - +
419D ALA* 1.3 57.5 + - - +
421D PHE* 3.4 5.4 + - - +
422D ARG* 3.1 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C ALA* 5.5 5.8 - - + +
415C GLY* 6.3 2.0 - - - -
415D GLY 2.9 19.4 + - - +
416D ALA 3.6 4.5 - - - +
418D GLU* 1.3 75.3 - - - +
420D SER* 1.3 60.6 + - - +
422D ARG* 4.1 12.8 - - - +
423D CYS* 2.9 37.8 + - - +
425D SER* 3.9 0.2 + - - -
510D ILE* 3.8 19.1 - - + -
525D MET* 4.2 17.0 - - + -
527D VAL* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D ALA 2.8 13.9 + - - -
417D VAL* 2.5 25.1 + - - -
419D ALA* 1.3 77.9 - - - +
421D PHE* 1.3 60.7 + - - +
424D CYS* 3.3 5.0 + - - -
425D SER* 2.9 43.0 + - - +
428D ILE* 3.7 25.7 - - - +
446D PRO* 4.0 9.5 - - - +
447D ARG 5.2 0.3 + - - -
448D ALA* 4.4 9.9 + - - +
510D ILE* 4.1 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D HIS* 4.0 25.8 - - + -
392D LEU* 3.6 28.9 - - + -
395D PHE* 3.8 24.7 - + + -
417D VAL* 3.2 41.1 + - + -
418D GLU* 3.8 6.1 - - - +
419D ALA 3.2 0.2 - - - -
420D SER* 1.3 81.7 + - - +
422D ARG* 1.3 63.2 + - - +
424D CYS* 3.4 17.4 + - - +
445D ARG 4.4 0.2 - - - -
446D PRO* 4.1 5.6 - - + -
447D ARG* 3.6 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ARG* 4.1 16.0 - - - +
405C THR* 3.8 26.2 + - - +
411C ALA* 4.4 20.7 + - - +
414C VAL* 3.5 29.4 - - - +
415C GLY* 4.7 5.3 - - - +
418C GLU* 2.4 42.8 + - - -
418D GLU* 3.1 31.9 + - - +
419D ALA* 3.3 10.4 + - - +
421D PHE* 1.3 79.6 - - - +
423D CYS* 1.3 65.2 + - - +
424D CYS* 3.7 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C THR 4.2 12.6 - - - +
406C SER* 5.4 9.4 - - - +
407C ASP 5.6 0.2 - - - -
411C ALA* 3.6 31.4 - - - -
419D ALA* 2.9 20.8 + - - +
422D ARG* 1.3 79.8 - - - +
424D CYS* 1.3 70.9 + - - +
425D SER* 3.4 13.7 + - - +
508D VAL* 4.1 20.1 - - + +
510D ILE* 4.7 2.9 - - - -
527D VAL* 4.3 15.9 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il